We've fixed this issue as well. We did a lot of improvements last month:
- adding video upload
- redirects after the video
- shortcode API compliance
WordPress 3.0 just happened to come out at the same time. A perfect storm, if you will. It took some time to reconcile all of the improvements and WordPress 3.0 to get things back to FV reliability. The older versions (easily downloadable at WordPress.org) did continue to work throughout though (without the new features).
We will be more careful with experimental versions going forward (we don't like to keep multiple versions open as it slows down development). We'll introduce one feature at a time.
Thanks for your help. As you know it's faster to submit bug reports and feature requests at our FV WordPress Flowplayer page.